/*
 * RateCovarianceStatistic.java
 *
 * Copyright (C) 2002-2006 Alexei Drummond and Andrew Rambaut
 *
 * This file is part of BEAST.
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership and licensing.
 *
 * BEAST is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 *  BEAST is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with BEAST; if not, write to the
 * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
 * Boston, MA  02110-1301  USA
 */

package dr.evomodel.tree;

import dr.evolution.tree.NodeRef;
import dr.evolution.tree.Tree;
import dr.inference.model.Statistic;
import dr.stats.DiscreteStatistics;
import dr.xml.*;
import dr.evomodel.branchratemodel.BranchRateModel;

/**
 * A statistic that tracks the covariance of rates on branches
 *
 * @version $Id: RateCovarianceStatistic.java,v 1.5 2005/07/11 14:06:25 rambaut Exp $
 *
 * @author Alexei Drummond
 *
 */
public class RateCovarianceStatistic extends Statistic.Abstract implements TreeStatistic {
	
	public static final String RATE_COVARIANCE_STATISTIC = "rateCovarianceStatistic";

	public RateCovarianceStatistic(String name, Tree tree, BranchRateModel branchRateModel) {
		super(name);
		this.tree = tree;
        this.branchRateModel = branchRateModel;

        int n = tree.getExternalNodeCount();
        childRate = new double[2*n-4];
        parentRate = new double[childRate.length];
    }

	public void setTree(Tree tree) { this.tree = tree; }
	public Tree getTree() { return tree; }
	
	public int getDimension() { return 1; }
	
	/** @return the height of the MRCA node. */
	public double getStatisticValue(int dim) {

	    int n = tree.getNodeCount();
        int index = 0;
        for (int i = 0; i < n; i++) {
            NodeRef child = tree.getNode(i);
            NodeRef parent = tree.getParent(child);
            if (parent != null & !tree.isRoot(parent)) {
                childRate[index] = branchRateModel.getBranchRate(tree, child);
                parentRate[index] = branchRateModel.getBranchRate(tree, parent);
                index += 1;
            }
        }
        return DiscreteStatistics.covariance(childRate, parentRate);
	}
	
	public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {
	
		public String getParserName() { return RATE_COVARIANCE_STATISTIC; }
	
		public Object parseXMLObject(XMLObject xo) throws XMLParseException {
			
			String name;
			if (xo.hasAttribute(NAME)) {
				name = xo.getStringAttribute(NAME);
			} else {
				name = xo.getId();
			}
			Tree tree = (Tree)xo.getChild(Tree.class);
            BranchRateModel branchRateModel = (BranchRateModel)xo.getChild(BranchRateModel.class);

			return new RateCovarianceStatistic(name, tree, branchRateModel);
		}
		
		//************************************************************************
		// AbstractXMLObjectParser implementation
		//************************************************************************

		public String getParserDescription() {
			return "A statistic that has as its value the covariance of parent and child branch rates";
		}

		public Class getReturnType() { return RateCovarianceStatistic.class; }

		public XMLSyntaxRule[] getSyntaxRules() { return rules; }
		
		private XMLSyntaxRule[] rules = new XMLSyntaxRule[] {
			new ElementRule(TreeModel.class),
            new ElementRule(BranchRateModel.class),
			new StringAttributeRule("name", "A name for this statistic primarily for the purposes of logging", true),
		};
	};

	private Tree tree = null;
    private BranchRateModel branchRateModel = null;
	private double[] childRate = null;
    private double[] parentRate = null;

}
